Starting phenix.real_space_refine on Sun Aug 24 13:05:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.map" model { file = "/net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iak_35306/08_2025/8iak_35306.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 12952 2.51 5 N 3356 2.21 5 O 3730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20154 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1231 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 576 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Restraints were copied for chains: E, F, H, G Time building chain proxies: 5.86, per 1000 atoms: 0.29 Number of scatterers: 20154 At special positions: 0 Unit cell: (171.72, 109.08, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3730 8.00 N 3356 7.00 C 12952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 796.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 53.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.846A pdb=" N ALA A 160 " --> pdb=" O GLN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.835A pdb=" N TYR A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 239 through 250 removed outlier: 4.166A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.701A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 389 through 406 removed outlier: 3.891A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.586A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 482 through 504 removed outlier: 3.710A pdb=" N GLU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.852A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.684A pdb=" N LYS B 89 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP B 92 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.662A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.703A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 4.358A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.771A pdb=" N LEU B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.615A pdb=" N ILE B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 399 through 415 removed outlier: 3.700A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.509A pdb=" N GLU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.034A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.788A pdb=" N ILE D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 141 through 148 removed outlier: 6.069A pdb=" N ASN D 146 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 174 Proline residue: D 162 - end of helix removed outlier: 4.380A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 192 through 196 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 53 through 74 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 157 through 160 removed outlier: 3.845A pdb=" N ALA E 160 " --> pdb=" O GLN E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.835A pdb=" N TYR E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 225 Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 239 through 250 removed outlier: 4.166A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 279 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.700A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.890A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 426 Processing helix chain 'E' and resid 450 through 459 removed outlier: 3.586A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 Processing helix chain 'E' and resid 482 through 504 removed outlier: 3.710A pdb=" N GLU E 486 " --> pdb=" O ILE E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.852A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.684A pdb=" N LYS F 89 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU F 91 " --> pdb=" O ASN F 88 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP F 92 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.662A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.703A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 4.358A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.551A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.771A pdb=" N LEU F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 350 removed outlier: 3.615A pdb=" N ILE F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.699A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 444 removed outlier: 3.509A pdb=" N GLU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 4.035A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 81 through 99 removed outlier: 3.788A pdb=" N ILE H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE H 88 " --> pdb=" O HIS H 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 91 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY H 99 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 141 through 148 removed outlier: 6.069A pdb=" N ASN H 146 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 174 Proline residue: H 162 - end of helix removed outlier: 4.380A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR H 172 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR H 173 " --> pdb=" O SER H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 Processing helix chain 'G' and resid 53 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 124 removed outlier: 7.229A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 148 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 211 removed outlier: 3.932A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.530A pdb=" N THR A 508 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.086A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.707A pdb=" N TYR B 147 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.867A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.617A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 124 removed outlier: 7.229A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.932A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 435 through 436 Processing sheet with id=AB3, first strand: chain 'E' and resid 444 through 445 removed outlier: 3.530A pdb=" N THR E 508 " --> pdb=" O LYS E 526 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.085A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.707A pdb=" N TYR F 147 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 218 through 222 removed outlier: 7.867A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.617A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6412 1.34 - 1.46: 4220 1.46 - 1.58: 9804 1.58 - 1.70: 2 1.70 - 1.81: 174 Bond restraints: 20612 Sorted by residual: bond pdb=" C4 PLP F 601 " pdb=" C5 PLP F 601 " ideal model delta sigma weight residual 1.390 1.493 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.493 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C2 PLP F 601 " pdb=" C3 PLP F 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 20607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 27525 2.43 - 4.86: 377 4.86 - 7.29: 48 7.29 - 9.72: 4 9.72 - 12.15: 4 Bond angle restraints: 27958 Sorted by residual: angle pdb=" N LYS B 366 " pdb=" CA LYS B 366 " pdb=" C LYS B 366 " ideal model delta sigma weight residual 111.14 121.13 -9.99 1.08e+00 8.57e-01 8.56e+01 angle pdb=" N LYS F 366 " pdb=" CA LYS F 366 " pdb=" C LYS F 366 " ideal model delta sigma weight residual 111.14 121.10 -9.96 1.08e+00 8.57e-01 8.50e+01 angle pdb=" N TYR B 58 " pdb=" CA TYR B 58 " pdb=" C TYR B 58 " ideal model delta sigma weight residual 111.71 118.03 -6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" N TYR F 58 " pdb=" CA TYR F 58 " pdb=" C TYR F 58 " ideal model delta sigma weight residual 111.71 117.99 -6.28 1.15e+00 7.56e-01 2.98e+01 angle pdb=" N ILE D 190 " pdb=" CA ILE D 190 " pdb=" C ILE D 190 " ideal model delta sigma weight residual 113.10 108.40 4.70 9.70e-01 1.06e+00 2.35e+01 ... (remaining 27953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11242 17.98 - 35.97: 905 35.97 - 53.95: 167 53.95 - 71.94: 22 71.94 - 89.92: 12 Dihedral angle restraints: 12348 sinusoidal: 4954 harmonic: 7394 Sorted by residual: dihedral pdb=" CA PHE A 256 " pdb=" C PHE A 256 " pdb=" N ASN A 257 " pdb=" CA ASN A 257 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PHE E 256 " pdb=" C PHE E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 157.50 -81.07 1 2.00e+01 2.50e-03 2.03e+01 ... (remaining 12345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3007 0.093 - 0.186: 155 0.186 - 0.279: 2 0.279 - 0.371: 0 0.371 - 0.464: 2 Chirality restraints: 3166 Sorted by residual: chirality pdb=" CA LYS B 366 " pdb=" N LYS B 366 " pdb=" C LYS B 366 " pdb=" CB LYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA LYS F 366 " pdb=" N LYS F 366 " pdb=" C LYS F 366 " pdb=" CB LYS F 366 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA TYR B 58 " pdb=" N TYR B 58 " pdb=" C TYR B 58 " pdb=" CB TYR B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3163 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 112 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ARG F 112 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG F 112 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG F 113 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 112 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ARG B 112 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG B 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 111 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C VAL B 111 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL B 111 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B 112 " -0.012 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 279 2.65 - 3.22: 18652 3.22 - 3.78: 28622 3.78 - 4.34: 39942 4.34 - 4.90: 69495 Nonbonded interactions: 156990 Sorted by model distance: nonbonded pdb=" O ASN A 407 " pdb=" N ALA A 409 " model vdw 2.093 3.120 nonbonded pdb=" O ASN E 407 " pdb=" N ALA E 409 " model vdw 2.094 3.120 nonbonded pdb=" OG SER A 417 " pdb=" O SER A 442 " model vdw 2.147 3.040 nonbonded pdb=" OG SER E 417 " pdb=" O SER E 442 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR E 460 " pdb=" OE1 GLU E 488 " model vdw 2.169 3.040 ... (remaining 156985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20614 Z= 0.239 Angle : 0.742 12.150 27958 Z= 0.443 Chirality : 0.046 0.464 3166 Planarity : 0.004 0.053 3552 Dihedral : 13.482 89.920 7588 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.17 % Favored : 93.60 % Rotamer: Outliers : 1.34 % Allowed : 1.07 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2514 helix: 1.42 (0.15), residues: 1182 sheet: -0.30 (0.36), residues: 216 loop : -1.66 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 174 TYR 0.019 0.001 TYR B 533 PHE 0.019 0.001 PHE E 256 TRP 0.010 0.001 TRP F 294 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00490 (20612) covalent geometry : angle 0.74218 (27958) hydrogen bonds : bond 0.17581 ( 1007) hydrogen bonds : angle 6.09063 ( 2877) Misc. bond : bond 0.06686 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.832 Fit side-chains REVERT: A 79 LYS cc_start: 0.7206 (tppt) cc_final: 0.6936 (tptm) REVERT: A 477 GLN cc_start: 0.7479 (mt0) cc_final: 0.7269 (mt0) REVERT: E 79 LYS cc_start: 0.7233 (tppt) cc_final: 0.6968 (tptm) REVERT: E 477 GLN cc_start: 0.7466 (mt0) cc_final: 0.7253 (mt0) outliers start: 30 outliers final: 10 residues processed: 264 average time/residue: 0.1249 time to fit residues: 51.9891 Evaluate side-chains 198 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 475 GLN Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS B 78 HIS B 143 ASN B 475 GLN E 421 HIS F 78 HIS F 143 ASN F 475 GLN G 60 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110336 restraints weight = 28657.954| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.84 r_work: 0.3122 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20614 Z= 0.121 Angle : 0.577 9.095 27958 Z= 0.306 Chirality : 0.042 0.178 3166 Planarity : 0.004 0.044 3552 Dihedral : 5.248 70.447 2780 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.91 % Rotamer: Outliers : 0.76 % Allowed : 6.69 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2514 helix: 1.81 (0.15), residues: 1210 sheet: 0.18 (0.33), residues: 248 loop : -1.44 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.019 0.001 TYR E 453 PHE 0.015 0.001 PHE A 256 TRP 0.009 0.001 TRP D 142 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00253 (20612) covalent geometry : angle 0.57665 (27958) hydrogen bonds : bond 0.04590 ( 1007) hydrogen bonds : angle 4.60027 ( 2877) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.605 Fit side-chains REVERT: A 79 LYS cc_start: 0.7554 (tppt) cc_final: 0.7261 (tptm) REVERT: E 79 LYS cc_start: 0.7594 (tppt) cc_final: 0.7309 (tptm) outliers start: 17 outliers final: 7 residues processed: 247 average time/residue: 0.1356 time to fit residues: 52.8028 Evaluate side-chains 226 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 50 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 241 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105485 restraints weight = 28919.801| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.83 r_work: 0.3041 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20614 Z= 0.219 Angle : 0.640 9.202 27958 Z= 0.337 Chirality : 0.045 0.160 3166 Planarity : 0.005 0.046 3552 Dihedral : 4.950 71.496 2758 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 1.34 % Allowed : 8.65 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2514 helix: 1.78 (0.15), residues: 1216 sheet: 0.17 (0.35), residues: 234 loop : -1.48 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 139 TYR 0.019 0.002 TYR B 510 PHE 0.030 0.002 PHE G 62 TRP 0.010 0.001 TRP F 294 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00543 (20612) covalent geometry : angle 0.63952 (27958) hydrogen bonds : bond 0.05913 ( 1007) hydrogen bonds : angle 4.57616 ( 2877) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.837 Fit side-chains REVERT: A 79 LYS cc_start: 0.7593 (tppt) cc_final: 0.7292 (tptm) REVERT: B 119 ASP cc_start: 0.8175 (t0) cc_final: 0.7710 (t0) REVERT: B 366 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8082 (mttt) REVERT: E 79 LYS cc_start: 0.7633 (tppt) cc_final: 0.7332 (tptm) REVERT: E 348 ASP cc_start: 0.8210 (m-30) cc_final: 0.7911 (m-30) REVERT: F 119 ASP cc_start: 0.8237 (t0) cc_final: 0.7782 (t0) REVERT: F 366 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8073 (mttt) REVERT: H 173 TYR cc_start: 0.6525 (p90) cc_final: 0.6299 (p90) outliers start: 30 outliers final: 22 residues processed: 228 average time/residue: 0.1445 time to fit residues: 52.1212 Evaluate side-chains 230 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108810 restraints weight = 28681.688| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.82 r_work: 0.3088 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20614 Z= 0.121 Angle : 0.547 8.512 27958 Z= 0.289 Chirality : 0.041 0.178 3166 Planarity : 0.004 0.044 3552 Dihedral : 4.782 70.978 2758 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 1.65 % Allowed : 9.68 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2514 helix: 2.00 (0.15), residues: 1206 sheet: 0.34 (0.33), residues: 242 loop : -1.35 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 174 TYR 0.014 0.001 TYR B 510 PHE 0.033 0.001 PHE G 62 TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00275 (20612) covalent geometry : angle 0.54716 (27958) hydrogen bonds : bond 0.04463 ( 1007) hydrogen bonds : angle 4.37701 ( 2877) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.790 Fit side-chains REVERT: A 79 LYS cc_start: 0.7535 (tppt) cc_final: 0.7287 (tptm) REVERT: A 348 ASP cc_start: 0.7964 (m-30) cc_final: 0.7590 (m-30) REVERT: B 18 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7896 (pp) REVERT: B 119 ASP cc_start: 0.8124 (t0) cc_final: 0.7648 (t0) REVERT: B 452 ASP cc_start: 0.8449 (m-30) cc_final: 0.7897 (t0) REVERT: B 530 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8680 (ttmp) REVERT: E 79 LYS cc_start: 0.7582 (tppt) cc_final: 0.7343 (tptm) REVERT: F 18 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (pp) REVERT: F 119 ASP cc_start: 0.8162 (t0) cc_final: 0.7681 (t0) REVERT: F 452 ASP cc_start: 0.8416 (m-30) cc_final: 0.7859 (t0) outliers start: 37 outliers final: 22 residues processed: 241 average time/residue: 0.1423 time to fit residues: 54.2493 Evaluate side-chains 238 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 214 optimal weight: 0.1980 chunk 202 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 173 optimal weight: 0.0010 chunk 183 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS E 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109257 restraints weight = 28491.702| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.82 r_work: 0.3095 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20614 Z= 0.120 Angle : 0.541 8.296 27958 Z= 0.284 Chirality : 0.041 0.178 3166 Planarity : 0.004 0.043 3552 Dihedral : 4.683 70.594 2758 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 1.65 % Allowed : 9.86 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2514 helix: 2.14 (0.15), residues: 1206 sheet: 0.37 (0.33), residues: 242 loop : -1.28 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 174 TYR 0.013 0.001 TYR F 510 PHE 0.025 0.001 PHE G 62 TRP 0.007 0.001 TRP F 294 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00278 (20612) covalent geometry : angle 0.54080 (27958) hydrogen bonds : bond 0.04250 ( 1007) hydrogen bonds : angle 4.26447 ( 2877) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.568 Fit side-chains REVERT: A 79 LYS cc_start: 0.7470 (tppt) cc_final: 0.7263 (tptm) REVERT: A 92 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6242 (mt-10) REVERT: B 18 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7910 (pp) REVERT: B 119 ASP cc_start: 0.8105 (t0) cc_final: 0.7610 (t0) REVERT: B 366 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8003 (mttt) REVERT: B 452 ASP cc_start: 0.8352 (m-30) cc_final: 0.7895 (t0) REVERT: B 530 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8704 (ttmp) REVERT: E 79 LYS cc_start: 0.7530 (tppt) cc_final: 0.7326 (tptm) REVERT: F 18 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7893 (pp) REVERT: F 119 ASP cc_start: 0.8133 (t0) cc_final: 0.7652 (t0) REVERT: F 366 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: F 452 ASP cc_start: 0.8346 (m-30) cc_final: 0.7886 (t0) REVERT: F 530 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8654 (ttmp) outliers start: 37 outliers final: 24 residues processed: 253 average time/residue: 0.1179 time to fit residues: 46.7374 Evaluate side-chains 242 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 3 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 464 GLN H 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110011 restraints weight = 28412.799| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.80 r_work: 0.3104 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20614 Z= 0.116 Angle : 0.540 8.129 27958 Z= 0.284 Chirality : 0.041 0.178 3166 Planarity : 0.004 0.042 3552 Dihedral : 4.621 69.864 2758 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 1.69 % Allowed : 10.39 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.17), residues: 2514 helix: 2.16 (0.15), residues: 1216 sheet: 0.39 (0.33), residues: 242 loop : -1.21 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 174 TYR 0.017 0.001 TYR D 173 PHE 0.027 0.001 PHE G 62 TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00267 (20612) covalent geometry : angle 0.54040 (27958) hydrogen bonds : bond 0.04112 ( 1007) hydrogen bonds : angle 4.22776 ( 2877) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.566 Fit side-chains REVERT: A 91 GLN cc_start: 0.7894 (mp10) cc_final: 0.7651 (mp10) REVERT: B 18 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7927 (pp) REVERT: B 107 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7401 (pt0) REVERT: B 119 ASP cc_start: 0.8098 (t0) cc_final: 0.7610 (t0) REVERT: B 366 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: B 452 ASP cc_start: 0.8332 (m-30) cc_final: 0.7907 (t0) REVERT: B 530 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (ttmp) REVERT: F 18 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7911 (pp) REVERT: F 107 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7413 (pt0) REVERT: F 119 ASP cc_start: 0.8093 (t0) cc_final: 0.7604 (t0) REVERT: F 366 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.7997 (mttt) REVERT: F 452 ASP cc_start: 0.8318 (m-30) cc_final: 0.7903 (t0) REVERT: F 530 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (ttmp) REVERT: H 173 TYR cc_start: 0.6742 (p90) cc_final: 0.6406 (p90) outliers start: 38 outliers final: 31 residues processed: 242 average time/residue: 0.1268 time to fit residues: 48.6193 Evaluate side-chains 246 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 178 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 29 optimal weight: 0.0980 chunk 240 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 155 optimal weight: 0.0470 chunk 159 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113770 restraints weight = 28487.380| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.81 r_work: 0.3168 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20614 Z= 0.095 Angle : 0.505 7.464 27958 Z= 0.264 Chirality : 0.040 0.186 3166 Planarity : 0.004 0.042 3552 Dihedral : 4.398 65.121 2758 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 1.34 % Allowed : 11.06 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.17), residues: 2514 helix: 2.27 (0.15), residues: 1218 sheet: 0.29 (0.31), residues: 266 loop : -1.06 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 174 TYR 0.012 0.001 TYR B 186 PHE 0.029 0.001 PHE G 62 TRP 0.006 0.001 TRP B 294 HIS 0.003 0.000 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00200 (20612) covalent geometry : angle 0.50458 (27958) hydrogen bonds : bond 0.03215 ( 1007) hydrogen bonds : angle 4.10321 ( 2877) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7881 (mp10) cc_final: 0.7649 (mp10) REVERT: B 18 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7902 (pp) REVERT: B 83 MET cc_start: 0.4312 (mmm) cc_final: 0.2890 (ptm) REVERT: B 107 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7422 (pt0) REVERT: B 119 ASP cc_start: 0.8071 (t0) cc_final: 0.7589 (t0) REVERT: B 452 ASP cc_start: 0.8335 (m-30) cc_final: 0.7835 (t0) REVERT: B 515 VAL cc_start: 0.9135 (t) cc_final: 0.8930 (t) REVERT: F 18 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7859 (pp) REVERT: F 83 MET cc_start: 0.4357 (mmm) cc_final: 0.2928 (ptm) REVERT: F 107 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7421 (pt0) REVERT: F 119 ASP cc_start: 0.8084 (t0) cc_final: 0.7591 (t0) REVERT: F 366 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: F 452 ASP cc_start: 0.8307 (m-30) cc_final: 0.7820 (t0) REVERT: F 515 VAL cc_start: 0.9129 (t) cc_final: 0.8921 (t) REVERT: F 530 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8641 (ttmp) REVERT: H 111 MET cc_start: 0.8204 (mmm) cc_final: 0.7254 (tmm) outliers start: 30 outliers final: 18 residues processed: 253 average time/residue: 0.1320 time to fit residues: 53.1069 Evaluate side-chains 238 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 119 optimal weight: 0.0060 chunk 78 optimal weight: 6.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN E 464 GLN F 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111658 restraints weight = 28580.875| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.80 r_work: 0.3134 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20614 Z= 0.106 Angle : 0.517 7.615 27958 Z= 0.270 Chirality : 0.040 0.176 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.385 67.880 2758 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 1.20 % Allowed : 11.86 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.17), residues: 2514 helix: 2.33 (0.15), residues: 1222 sheet: 0.60 (0.33), residues: 242 loop : -1.02 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 174 TYR 0.013 0.001 TYR B 510 PHE 0.028 0.001 PHE G 62 TRP 0.005 0.001 TRP B 294 HIS 0.003 0.000 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00239 (20612) covalent geometry : angle 0.51706 (27958) hydrogen bonds : bond 0.03620 ( 1007) hydrogen bonds : angle 4.06806 ( 2877) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.860 Fit side-chains REVERT: A 91 GLN cc_start: 0.7890 (mp10) cc_final: 0.7668 (mp10) REVERT: B 18 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 83 MET cc_start: 0.4496 (mmm) cc_final: 0.3041 (ptm) REVERT: B 107 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7442 (pt0) REVERT: B 119 ASP cc_start: 0.8107 (t0) cc_final: 0.7618 (t0) REVERT: B 366 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.7810 (mttt) REVERT: B 452 ASP cc_start: 0.8286 (m-30) cc_final: 0.7828 (t0) REVERT: F 18 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7852 (pp) REVERT: F 83 MET cc_start: 0.4514 (mmm) cc_final: 0.3026 (ptm) REVERT: F 107 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7442 (pt0) REVERT: F 119 ASP cc_start: 0.8106 (t0) cc_final: 0.7615 (t0) REVERT: F 366 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.7827 (mttt) REVERT: F 452 ASP cc_start: 0.8263 (m-30) cc_final: 0.7815 (t0) REVERT: F 530 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8668 (ttmp) REVERT: G 59 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7972 (mt) outliers start: 27 outliers final: 20 residues processed: 233 average time/residue: 0.1455 time to fit residues: 54.7525 Evaluate side-chains 235 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 208 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110040 restraints weight = 28234.896| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.89 r_work: 0.3108 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20614 Z= 0.123 Angle : 0.541 7.866 27958 Z= 0.283 Chirality : 0.041 0.171 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.477 69.962 2758 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.83 % Rotamer: Outliers : 1.43 % Allowed : 11.82 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.17), residues: 2514 helix: 2.30 (0.15), residues: 1218 sheet: 0.61 (0.33), residues: 242 loop : -1.04 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 174 TYR 0.014 0.001 TYR F 510 PHE 0.026 0.001 PHE G 62 TRP 0.006 0.001 TRP B 294 HIS 0.003 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00290 (20612) covalent geometry : angle 0.54148 (27958) hydrogen bonds : bond 0.04020 ( 1007) hydrogen bonds : angle 4.12454 ( 2877) Misc. bond : bond 0.00001 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.810 Fit side-chains REVERT: A 91 GLN cc_start: 0.7908 (mp10) cc_final: 0.7672 (mp10) REVERT: A 348 ASP cc_start: 0.7785 (m-30) cc_final: 0.7556 (m-30) REVERT: B 18 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7918 (pp) REVERT: B 107 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7464 (pt0) REVERT: B 119 ASP cc_start: 0.8090 (t0) cc_final: 0.7633 (t0) REVERT: B 366 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.7973 (mttt) REVERT: B 452 ASP cc_start: 0.8366 (m-30) cc_final: 0.7904 (t0) REVERT: F 18 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7921 (pp) REVERT: F 107 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7470 (pt0) REVERT: F 119 ASP cc_start: 0.8145 (t0) cc_final: 0.7664 (t0) REVERT: F 366 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: F 452 ASP cc_start: 0.8324 (m-30) cc_final: 0.7882 (t0) REVERT: F 530 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (ttmp) REVERT: G 59 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7981 (mt) outliers start: 32 outliers final: 21 residues processed: 233 average time/residue: 0.1191 time to fit residues: 44.3968 Evaluate side-chains 233 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 158 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 90 optimal weight: 0.0030 chunk 14 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 242 optimal weight: 0.0060 chunk 212 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112730 restraints weight = 28527.367| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.79 r_work: 0.3161 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20614 Z= 0.099 Angle : 0.518 7.894 27958 Z= 0.271 Chirality : 0.040 0.179 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.375 67.662 2758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 1.07 % Allowed : 12.04 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.17), residues: 2514 helix: 2.31 (0.15), residues: 1220 sheet: 0.65 (0.32), residues: 242 loop : -0.95 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 174 TYR 0.015 0.001 TYR H 173 PHE 0.056 0.001 PHE C 62 TRP 0.005 0.001 TRP B 294 HIS 0.003 0.000 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00216 (20612) covalent geometry : angle 0.51820 (27958) hydrogen bonds : bond 0.03406 ( 1007) hydrogen bonds : angle 4.07315 ( 2877) Misc. bond : bond 0.00009 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.626 Fit side-chains REVERT: A 91 GLN cc_start: 0.7905 (mp10) cc_final: 0.7678 (mp10) REVERT: B 18 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7889 (pp) REVERT: B 83 MET cc_start: 0.4451 (mmm) cc_final: 0.3078 (ptm) REVERT: B 107 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7475 (pt0) REVERT: B 119 ASP cc_start: 0.8045 (t0) cc_final: 0.7581 (t0) REVERT: B 366 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.7795 (mttt) REVERT: B 452 ASP cc_start: 0.8286 (m-30) cc_final: 0.7830 (t0) REVERT: E 79 LYS cc_start: 0.7339 (tppt) cc_final: 0.6926 (tptm) REVERT: E 489 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 18 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7879 (pp) REVERT: F 83 MET cc_start: 0.4485 (mmm) cc_final: 0.3160 (ptm) REVERT: F 107 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7460 (pt0) REVERT: F 119 ASP cc_start: 0.8109 (t0) cc_final: 0.7629 (t0) REVERT: F 366 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.7804 (mttt) REVERT: F 452 ASP cc_start: 0.8267 (m-30) cc_final: 0.7822 (t0) REVERT: F 530 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8627 (ttmp) REVERT: G 59 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 24 outliers final: 15 residues processed: 236 average time/residue: 0.1117 time to fit residues: 42.7270 Evaluate side-chains 234 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 169 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 213 optimal weight: 6.9990 chunk 146 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS E 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110470 restraints weight = 28407.141| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.81 r_work: 0.3121 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20614 Z= 0.122 Angle : 0.543 7.685 27958 Z= 0.283 Chirality : 0.041 0.171 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.393 70.503 2754 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.67 % Rotamer: Outliers : 1.16 % Allowed : 12.04 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.17), residues: 2514 helix: 2.31 (0.15), residues: 1218 sheet: 0.66 (0.32), residues: 242 loop : -1.00 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 174 TYR 0.014 0.001 TYR F 510 PHE 0.055 0.001 PHE C 62 TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00288 (20612) covalent geometry : angle 0.54276 (27958) hydrogen bonds : bond 0.03955 ( 1007) hydrogen bonds : angle 4.10075 ( 2877) Misc. bond : bond 0.00001 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5042.54 seconds wall clock time: 86 minutes 59.87 seconds (5219.87 seconds total)